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Question: Beginner question: differences/advantages of Bioconductor for sequence analysis
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gravatar for vasvale
5 weeks ago by
vasvale0
vasvale0 wrote:

I'd appreciate, as a beginner, if you could explain what, if any, differences are provided by Bioconductor workflows for alignment, variant calling and annotation of NGS exome studies. That is comparing to tools available in Galaxy or from Broad BWA/ GATK and versus other annotations tools. This info may be useful in the Home page.

Thanks

Vasvale

 

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by vasvale0

An alternate viewpoint is that as a beginner, it is in your best interest to educate yourself as to the similarities and differences between the different choices available to you and then make that choice yourself. That way you become not a beginner, and you have some idea of the capabilities that are on offer.

Anyway, do note that Bioconductor is a large project that encompasses way more workflows than variant calling for WGS exome studies. While we could hypothetically put something on the home page to compare and contrast our tools vs whatever else is out there for that one workflow, what about the hundreds of other things you can do with Bioconductor?
 

ADD REPLYlink written 5 weeks ago by James W. MacDonald42k

I see that there are many tools but I am interested in alignment and variant calling. I would not want to spend time in any single site available if I could just know to begin with, if the tools are different or not. So for instance, if I understand it correctly,  the alignment tool here is BWA so It's the same of what is available in Galaxy or in the Broad apps list?

ADD REPLYlink written 5 weeks ago by vasvale0
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